MolNFT v1 · #50742 · protein

Solution structure of the plant homeodomain (phd) of the E3 sumo ligase SIZ1 from rice

2RSD · E3 sumo-protein ligase SIZ1: “Solution structure of the plant homeodomain (phd) of the E3 sumo ligase SIZ1 from rice”. Solution nmr, 1 ligand (ZN), 1 pocket (best druggability 0.31). MolNFT v1 #50742 on GenesisL1: 3D structure…

PDB: 2RSD
Type: protein
Length: 68 residues
Chains: 1
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 sumo-protein ligase SIZ1
EC: 6.3.2.-
UniProt: Q6L4L4
Ligands: ZN
Pockets: 1 · best druggability 0.31

Structure

solution nmr · 1 distinct chain · 10% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	E3 sumo-protein ligase SIZ1 (EC 6.3.2.-)	protein	68	10% helix, 13% strand	Q6L4L4

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	62	0.31	0.75	15	empty

Compared structures

2RSD · Solution structure of the plant homeodomain (PHD) of the E3 SUMO ligase Siz1 from rice · the same entry in another collection · chain A against A, TM-score 1.00
Q6L4L4 · AlphaFold monomer V2.0 prediction for E3 sumo-protein ligase SIZ1 (Q6L4L4) · a predicted model of the same protein · chain A against A, TM-score 0.77

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q6L4L4
Elsewhere: RCSB PDB 2RSD · PDBe 2RSD · UniProt Q6L4L4

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